clang error Mac OS Catalina 10.15.5

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Jorge Guevara

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Sep 1, 2020, 8:27:41 PM9/1/20
to hydromad users
Hi, 
I am trying to install Hydromat on Mac OS Catalina under conda with

install.packages("hydromad", repos="http://hydromad.catchment.org", lib="/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library")

I have the following error message:


* installing *source* package ‘hydromad’ ...

** using staged installation

...

ld: warning: -pie being ignored. It is only used when linking a main executable

ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libSystem.tbd' for architecture x86_64

clang-10: error: linker command failed with exit code 1 (use -v to see invocation)

make: *** [/Users/jorgegd/anaconda3/envs/weathergen/lib/R/share/make/shlib.mk:6: hydromad.dylib] Error 1

ERROR: compilation failed for package ‘hydromad’

Do you have any turnaround for this.  I will appreciate any help on this


Best

Jorge Guevara

unread,
Sep 1, 2020, 8:32:44 PM9/1/20
to hydromad users

Below is the complete output

> install.packages("hydromad", repos="http://hydromad.catchment.org", lib="/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library")

trying URL 'http://hydromad.catchment.org/src/contrib/hydromad_0.9-26.tar.gz'

Content type 'text/javascript' length 1373896 bytes (1.3 MB)

==================================================

downloaded 1.3 MB


* installing *source* package ‘hydromad’ ...

** using staged installation

** libs

x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c RcppExports.cpp -o RcppExports.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c awbm.c -o awbm.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c bucket.c -o bucket.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c cmd.c -o cmd.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c filters.c -o filters.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c fland1.c -o fland1.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c gr4j.c -o gr4j.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c hydromad-init.c -o hydromad-init.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c inversefilter.c -o inversefilter.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c riv.c -o riv.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c sacramento.c -o sacramento.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c sacramento_state.c -o sacramento_state.o

x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c simhyd.cpp -o simhyd.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c snow.c -o snow.o

x86_64-apple-darwin13.4.0-clang -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/include" -DNDEBUG  -I"/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9  -I/Users/jorgegd/anaconda3/envs/weathergen/include  -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jorgegd/anaconda3/envs/weathergen/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/jorgegd/anaconda3/envs/weathergen=/usr/local/src/conda-prefix  -c swimp.c -o swimp.o

x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/jorgegd/anaconda3/envs/weathergen/lib/R/lib -Wl,-dead_strip_dylibs -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/jorgegd/anaconda3/envs/weathergen/lib -L/Users/jorgegd/anaconda3/envs/weathergen/lib -o hydromad.dylib RcppExports.o awbm.o bucket.o cmd.o filters.o fland1.o gr4j.o hydromad-init.o inversefilter.o riv.o sacramento.o sacramento_state.o simhyd.o snow.o swimp.o -L/Users/jorgegd/anaconda3/envs/weathergen/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation

ld: warning: -pie being ignored. It is only used when linking a main executable

ld: unsupported tapi file type '!tapi-tbd' in YAML file '/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libSystem.tbd' for architecture x86_64

clang-10: error: linker command failed with exit code 1 (use -v to see invocation)

make: *** [/Users/jorgegd/anaconda3/envs/weathergen/lib/R/share/make/shlib.mk:6: hydromad.dylib] Error 1

ERROR: compilation failed for package ‘hydromad’

* removing ‘/Users/jorgegd/anaconda3/envs/weathergen/lib/R/library/hydromad’


The downloaded source packages are in

‘/private/var/folders/c4/3d2nppsx3m7c0cfckqr8661m0000gp/T/RtmpAtqXMK/downloaded_packages’

Updating HTML index of packages in '.Library'

Making 'packages.html' ... done

Warning message:

In install.packages("hydromad", repos = "http://hydromad.catchment.org",  :

  installation of package ‘hydromad’ had non-zero exit status

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